chr10-98400642-T-C

Position:

• chr10-98400642-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_032709.3(PYROXD2):​c.316-385A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.507 in 151,938 control chromosomes in the GnomAD database, including 21,994 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.51 (21994 hom., cov: 32)
• Consequence: PYROXD2 NM_032709.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.50

Genes affected

PYROXD2 (HGNC:23517): (pyridine nucleotide-disulphide oxidoreductase domain 2) Predicted to enable oxidoreductase activity. Involved in mitochondrion organization. Located in mitochondrial matrix. [provided by Alliance of Genome Resources, Apr 2022]

PYROXD2 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.774 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PYROXD2	NM_032709.3	c.316-385A>G		intron_variant		ENST00000370575.5	NP_116098.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PYROXD2	ENST00000370575.5	c.316-385A>G		intron_variant		1	NM_032709.3	ENSP00000359607.4
PYROXD2	ENST00000483923.5	n.1218-385A>G		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.507 AC: 76951 AN: 151818 Hom.: 21938 Cov.: 32

Gnomad AFR AF: 0.780

Gnomad AMI AF: 0.412

Gnomad AMR AF: 0.479

Gnomad ASJ AF: 0.471

Gnomad EAS AF: 0.526

Gnomad SAS AF: 0.544

Gnomad FIN AF: 0.431

Gnomad MID AF: 0.434

Gnomad NFE AF: 0.359

Gnomad OTH AF: 0.465

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.507 AC: 77065 AN: 151938 Hom.: 21994 Cov.: 32 AF XY: 0.512 AC XY: 38041 AN XY: 74242

Gnomad4 AFR AF: 0.781

Gnomad4 AMR AF: 0.479

Gnomad4 ASJ AF: 0.471

Gnomad4 EAS AF: 0.527

Gnomad4 SAS AF: 0.543

Gnomad4 FIN AF: 0.431

Gnomad4 NFE AF: 0.359

Gnomad4 OTH AF: 0.462

Alfa AF: 0.435 Hom.: 1962

Bravo AF: 0.519

Asia WGS AF: 0.552 AC: 1916 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.73
DANN	Benign	0.38

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs6584194; hg19: chr10-100160399;